Efficient space-time codes from cyclic division algebras

An overview of space-time code construction based on cyclic division algebras (CDA) is presented. Applications of such space-time codes to the construction of codes optimal under the diversity-multiplexing gain (D-MG) tradeoff, to the construction of the so-called perfect space-time codes, to the construction of optimal space-time codes for the ARQ channel as well as to the construction of codes optimal for the cooperative relay network channel are discussed. We also present a construction of optimal codes based on CDA for a class of orthogonal amplify and forward (OAF) protocols for the cooperative relay network

Self-Assembling Peptides: From Molecules to Nanobiomaterials

Abstract | Molecular self-assembly plays a vital role in the construction of various nanostructures using the ‘bottom-up’ approach. Peptides have been considered important bio-molecular building blocks for different nanoscale structures as they are biocompatible, biodegradable, generally non-toxic and can be attuned to environmental responses like pH, temperature, salt concentration and others. Peptide based nanostructures can offer various wonderful biological applications in tissue engineering, cell culture, regenerative medicine and drug delivery. In this review, the construction of short peptide-based different nanostructures including nanotubes, nanovesicles and nanofibers, short peptide-based nanoporous materials, short peptide-based nanofibrous hydrogels and nanovesicles for various biological applications has been discussed. Moreover, morphological transformations from one nanoscopic structure to an other type of nanostructure (e.g., nanotubes to nanovesicles) are also clearly discussed in this review.

NMRof peptides

Developments and applications of NMR spectroscopy especially with biomolecules has taken big strides over the decades. This review gives a brief overview of peptide analysis by NMR as carried out in the author’s laboratory. A brief introduction to peptide biomolecules and NMR useful parameters are discussed in the beginning. This is followed by diagnostics features observed in NMR for identification of secondary structures. It further goes on to show how a three dimensional structure could be obtained by all-important NOE and hydrogen bond information. Use of heteronuclear experiments, which could be done at natural abundance is also highlighted in getting more details of peptide structures.Applications using Solid state NMR at natural abundance in connecting peptide solution and x-ray structures is demonstrated with couple of examples.

Gap model of one-way cyclic lateral load on vertical files in soft clay

For the analysis and design of pile foundation used for coastal structures the prediction of cyclic response, which is influenced by the nonlinear behavior, gap (pile soil separation) and degradation (reduction in strength) of soil becomes necessary. To study the effect of the above parameters a nonlinear cyclic load analysis program using finite element method is developed, incorporating the proposed gap and degradation model and adopting an incremental-iterative procedure. The pile is idealized using beam elements and the soil by number of elastoplastic sub-element springs at each node. The effect of gap and degradation on the load-deflection behavior. elasto-plastic sub-element and resistance of the soil at ground-line have been clearly depicted in this paper.

Nonlinear cyclic load analysis for lateral response of batter piles in soft clay with a rigorous degradation model

Nonlinear analysis of batter piles in soft clay is performed using the finite element technique. As the batter piles are not only governed by lateral load but also axial load, the effect of P- Delta moment and geometric stiffness matrix is included in the analysis. For implementing the nonlinear soil behavior, reduction in soil strength (degradation), and formation of gap with number of load cycles, a numerical model is developed where a hyperbolic relation is adopted for the soil in static condition and hyperbolic relation considering degradation and gap for cyclic load condition. The numerical model is validated with published experimental results for cyclic lateral loading and the hysteresis loops are developed to predict the load-deflection behavior and soil resistance behavior during consecutive cycles of loading. This paper highlights the importance of a rigorous degradation model for subsequent cycles of loading on the pile-soil system by a hysteretic representation.

Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design

Most HIV-1 broadly neutralizing antibodies are directed against the gp120 subunit of the env surface protein. Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones. Some cryo-electron tomography studies have suggested that the V1V2 loop regions of gp120 are located close to the trimer interface. We have therefore designed cyclically permuted variants of gp120 with and without the h-CMP and SUMO2a trimerization domains inserted into the V1V2 loop. h-CMP-V1cyc is one such variant in which residues 153 and 142 are the N- and C-terminal residues, respectively, of cyclically permuted gp120 and h-CMP is fused to the N-terminus. This molecule forms a trimer under native conditions and binds CD4 and the neutralizing CD4bs antibodies b12 with significantly higher affinity than wild-type gp120. It binds non-neutralizing CD4bs antibody F105 with lower affinity than gp120. A similar derivative, h-CMP-V1cycl, bound the V1V2 loop-directed broadly neutralizing antibodies PG9 and PG16 with similar to 20-fold higher affinity than wild-type JRCSF gp120. These cyclic permutants of gp120 are properly folded and are potential immunogens. The data also support env models in which the V1V2 loops are proximal to the trimer interface.

Thermal Management of Electronics Using PCM-Based Heat Sink Subjected to Cyclic Heat Load

Designing a heat sink based on a phase change material (PCM) under cyclic loading is a critical issue. For cyclic operation, it is required that the fraction of the PCM melting during the heating cycle should completely resolidify during the cooling period, so that that thermal storage unit can be operated for an unlimited number of cycles. Accordingly, studies are carried out to find the parameters influencing the behavior of a PCM under cyclic loading. A number of parameters are identified in the process, the most important ones being the duty cycle and heat transfer coefficient (h) for cooling. The required h or the required cooling period for complete resolidification for infinite cyclic operation of a conventional PCM-based heat sink is found to be very high and unrealistic with air cooling from the surface. To overcome this problem, the conventional design is modified where h and the area exposed to heat transfer can be independently controlled. With this arrangement, the enhanced area provided for cooling keeps h within realistic limits. Analytical investigation is carried out to evaluate the thermal performance of this modified PCM-based heat sink in comparison to those with conventional designs. Experiments are also performed on both the conventional and the modified PCM-based heat sinks to validate the new findings.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Spontaneous self-assembly of designed cyclic dipeptide (Phg-Phg) into two-dimensional nano- and mesosheets

In this study, we present the spontaneous self-assembly of designed simplest aromatic cyclic dipeptides of (L-Phg-L-Phg) and (D-Phg-L-Phg) to form highly stable two-dimensional (2D) nano- and mesosheets with large lateral surface area. Various microscopy data revealed that the morphology of 2D mesosheets resembles the hierarchical natural materials with layered structure. Solution and solid-state NMR studies on cyclo(L-Phg-L-Phg) revealed the presence of strong (N-H-O) hydrogen-bonded molecular chains supported by aromatic pi-pi interactions to form 2D mesosheets. Interestingly, cyclo(D-Phg-L-Phg) self-assembles to form single-crystalline as well as non-crystalline 2D rhomboid sheets with large lateral dimension. X-ray diffraction analysis revealed the stacking of (N-H-O) hydrogen-bonded molecular layers along c-axis supported by aromatic pi-pi interactions. The thermogravimetric analysis shows two transitions with overall high thermal stability attributed to layered hierarchy found in 2D mesosheets.

Helix and hairpin nucleation in short peptides using centrally positioned conformationally constrained dipeptide segments

The effect of incorporation of a centrally positioned Ac(6)c-Xxx segment where Xxx = (L)Val/(D)Val into a host oligopeptide composed of L-amino acid residues has been investigated. Studies of four designed octapeptides Boc-Leu-Phe-Val-Ac(6)c-Xxx-Leu-Phe-Val-OMe (Xxx = (D)Val 1, (L)Val 2) Boc-Leu-Val-Val-Ac(6)c-Xxx-Leu-Val-Val-OMe (Xxx = (D)Val 3, (L)Val 4) are reported. Diagnostic nuclear Overhouse effects characteristic of hairpin conformations are observed for Xxx = (D)Val peptides (1 and 3) while continuous helical conformation characterized by sequential NiH <-> Ni+1H NOEs are favored for Xxx = (L)Val peptides (2 and 4) in methanol solutions. Temperature co-efficient of NH chemical shifts are in agreement with distinctly different conformational preferences upon changing the configuration of the residue at position 5. Crystal structures of peptides 2 and 4 (Xxx = (L)Val) establish helical conformations in the solid state, in agreement with the structures deduced from NMR data. The results support the design principle that centrally positioned type I beta-turns may be used to nucleate helices in short peptides, while type I' beta-turns can facilitate folding into beta-hairpins.

beta-Turn Analogues in Model a ss-Hybrid Peptides: Structural Characterization of Peptides Containing ss 2,2Ac6c and ss 3,3Ac6c Residues

The effect of gem-dialkyl substituents on the backbone conformations of beta-amino acid residues in peptides has been investigated by using four model peptides: Boc-Xxx-beta 2,2Ac6c(1-aminomethylcyclohexanecarboxylic acid)-NHMe (Xxx=Leu (1), Phe (2); Boc=tert-butyloxycarbonyl) and Boc-Xxx-beta 3,3Ac6c(1-aminocyclohexaneacetic acid)-NHMe (Xxx=Leu (3), Phe (4)). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc-Leu-beta 2,2Ac6c-NHMe (1) established a C11 hydrogen-bonded turn in the a beta-hybrid sequence. The observed torsion angles (a(similar to-60 degrees, similar to-30 degrees), beta(similar to-90 degrees, similar to 60 degrees, similar to-90 degrees)) corresponded to a C11 helical turn, which was a backbone-expanded analogue of the type III beta turn in aa sequences. The crystal structure of the peptide Boc-Phe-beta 3,3Ac6c-NHMe (4) established a C11 hydrogen-bonded turn with distinctly different backbone torsion angles (a(similar to-60 degrees, similar to 120 degrees), beta(similar to 60 degrees, ?60 degrees, similar to-60 degrees)), which corresponded to a backbone-expanded analogue of the type II beta turn observed in aa sequences. In peptide 4, the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these a beta-hybrid sequences.

Synthesis and Characterization of a Fluorescent Analogue of Cyclic di-GMP

Cyclic di-GMP (c-di-GMP), a ubiquitous bacterial second messenger, has emerged as a key controller of several biological processes. Numbers of reports that deal with the mechanistic aspects of this second messenger have appeared in the literature. However, the lack of a reporter tag attached to the c-di-GMP at times limits the understanding of further details. In this study, we have chemically coupled N-methylisatoic anhydride (MANT) with c-di-GMP, giving rise to Mant-(c-di-GMP) or MANT-CDG. We have characterized the chemical and physical properties and spectral behavior of MANT-CDG. The fluorescence of MANT-CDG is sensitive to changes in the microenvironment, which helped us study its interaction with three different c-di-GMP binding proteins (a diguanylate cyclase, a phosphodiesterase, and a PilZ domain-containing protein). In addition, we have shown here that MANT-CDG can inhibit diguanylate cyclase activity; however, it is hydrolyzed by c-di-GMP specific phosphodiesterase. Taken together, our data suggest that MANT-CDG behaves like native c-di-GMP, and this study raises the possibility that MANT-CDG will be a valuable research tool for the in vitro characterization of c-di-GMP signaling factors.

Cyclic AMP-induced Conformational Changes in Mycobacterial Protein Acetyltransferases

The activities of a number of proteins are regulated by the binding of cAMP and cGMP to cyclic nucleotide binding (CNB) domains that are found associated with one or more effector domains with diverse functions. Although the conserved architecture of CNB domains has been extensively studied by x-ray crystallography, the key to unraveling the mechanisms of cAMP action has been protein dynamics analyses. Recently, we have identified a novel cAMP-binding protein from mycobacteria, where cAMP regulates the activity of an associated protein acetyltransferase domain. In the current study, we have monitored the conformational changes that occur upon cAMP binding to the CNB domain in these proteins, using a combination of bioluminescence resonance energy transfer and amide hydrogen/deuterium exchange mass spectrometry. Coupled with mutational analyses, our studies reveal the critical role of the linker region (positioned between the CNB domain and the acetyltransferase domain) in allosteric coupling of cAMP binding to activation of acetyltransferase catalysis. Importantly, major differences in conformational change upon cAMP binding were accompanied by stabilization of the CNB and linker domain alone. This is in contrast to other cAMP-binding proteins, where cyclic nucleotide binding has been shown to involve intricate and parallel allosteric relays. Finally, this powerful convergence of results from bioluminescence resonance energy transfer and hydrogen/deuterium exchange mass spectrometry reaffirms the power of solution biophysical tools in unraveling mechanistic bases of regulation of proteins in the absence of high resolution structural information.

Structural characterization of backbone-expanded helices in hybrid peptides: (αγ) n and (αβ) n sequences with unconstrained β and γ homologues of L-Val

Learning your αβγ's: The diversity of hydrogen-bonding patterns in backbone-expanded hybrid helices is shown by crystal-structure determination of several oligomeric peptides (see scheme; C=gray; H=white; O=red; N=blue). C 12 helices were observed in the αγ peptide series for n=2-8. In comparison, the αα peptide and αβ peptide sequences show C 10 and mixed C 14/C 15 helices, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.